Contacts of the strand formed by residues 138 - 145 (chain A) in PDB entry 1LKF
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LEU* 3.9 33.4 - - + -
20A LYS* 5.8 0.9 - - - -
39A ASN* 3.5 37.5 - - + -
41A ILE* 4.0 22.4 - - + -
52A VAL* 3.6 27.6 - - + -
114A LEU* 4.8 5.2 - - + -
115A GLY* 3.5 1.6 - - - -
116A TYR* 2.9 37.6 + - + +
136A THR* 3.5 5.6 + - - -
137A ALA* 1.3 82.0 - - - +
139A SER* 1.3 72.5 + - - +
140A GLU* 3.5 34.5 - - + -
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Residues in contact with SER 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A THR* 3.8 19.9 - - - +
114A LEU 3.4 6.9 + - - -
115A GLY* 4.6 2.8 - - - -
136A THR* 4.5 10.4 + - - -
138A PHE* 1.3 89.5 - - - +
140A GLU* 1.3 70.1 + - - +
141A THR* 5.7 0.7 - - - +
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Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LYS* 4.8 11.6 + - - -
37A THR* 5.6 2.4 - - - +
39A ASN* 4.5 9.2 + - - +
52A VAL* 4.8 0.7 - - + -
54A LYS* 3.3 32.1 + - + +
113A THR* 3.4 4.9 - - - +
114A LEU 2.8 36.1 + - - +
138A PHE* 3.5 31.5 - - + -
139A SER* 1.3 74.0 - - - +
141A THR* 1.3 86.5 + - - +
226A LEU* 4.0 27.8 - - + +
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Residues in contact with THR 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LYS* 3.0 33.6 + - - +
112A ASN 3.3 8.1 - - - +
113A THR* 3.8 21.3 - - + +
128A LEU* 3.9 30.8 - - + +
139A SER* 5.7 0.9 - - - +
140A GLU* 1.3 87.1 + - - +
142A ILE* 1.3 65.8 + - - +
143A ASN* 4.3 1.8 - - - +
224A GLU* 4.4 1.1 + - - -
226A LEU* 4.3 2.0 - - - +
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Residues in contact with ILE 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LYS* 5.1 2.0 - - - -
100A ALA* 4.1 8.1 - - + +
101A PRO* 3.9 15.0 - - + -
110A VAL* 3.6 32.1 - - + +
111A GLN* 3.3 4.0 - - - -
112A ASN* 3.1 53.6 + - + +
128A LEU* 3.9 2.9 - - - +
141A THR* 1.3 73.5 - - - +
143A ASN* 1.3 62.2 + - - +
144A TYR* 3.9 9.0 - - + -
224A GLU* 3.2 32.8 - - + +
225A PHE* 3.8 1.3 - - - -
226A LEU* 3.4 39.7 - - + +
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Residues in contact with ASN 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLN* 3.0 24.4 + - - +
110A VAL 3.2 3.4 - - - -
111A GLN* 3.1 33.4 - - - +
128A LEU* 4.3 13.2 - - + -
141A THR* 5.5 2.2 - - - +
142A ILE* 1.3 78.5 - - - +
144A TYR* 1.3 63.2 + - - +
222A ASN 4.8 0.5 - - - +
224A GLU* 2.7 33.7 + - - +
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Residues in contact with TYR 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A PRO* 3.6 6.8 - - - +
109A GLN* 3.4 9.3 - - - +
110A VAL* 2.9 56.0 + - + +
142A ILE* 3.9 16.4 - - + -
143A ASN* 1.3 77.5 - - - +
145A LYS* 1.3 61.9 + - - +
146A GLN* 3.7 10.5 - - + -
151A THR* 2.8 38.9 + - - +
221A PHE* 3.6 25.8 - + + -
222A ASN 3.5 22.2 - - - +
224A GLU* 3.4 33.9 - - + +
225A PHE* 3.5 19.3 - + - -
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Residues in contact with LYS 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PHE* 3.4 12.3 - - - +
109A GLN* 3.6 26.8 + - - +
144A TYR* 1.3 74.7 - - - +
146A GLN* 1.3 62.6 + - - +
147A GLU* 4.7 20.0 - - + +
215A LEU* 6.3 2.6 - - - +
216A LEU* 3.9 16.8 - - - +
221A PHE* 3.9 10.4 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il